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On a far away planet, spacemen Olimar and Louie are at a Farewell Party for themselves. All their friends and family are gathered to say goodbye to them as the next day they will take off to explore the depths of space. At the party, a stranger confronts the two and tells them about an ancient prophecy about a dark force that threatens their existence, but Olimar just thinks he's crazy and slowly walks away.
The next day, Olimar and Louie get suited up and take off in the spaceship, into parts unknown. However, as they leave the planet's atmosphere the spaceship starts malfunctioning and making beeping noises. Suddenly, the hull of the ship breaks open and Louie starts to get sucked out. Olimar grabs Louie's hand but the pull is too strong and Louie flies off into deep space, as Olimar speeds off in the rocket, still holding on for dear life. Olimar faints from the sheer terror. Back on their planet, the head of the space program reveals to the public that they have lost contact with the ship and for all they know Olimar and Louie are lost.
On a distant planet, the ship lands down and crashes in a huge grassy field. Olimar wakes up and climbs out of the ship, and is greeted by a tribe of small carrot-like creatures known as Pikmin. There are only three different Pikmin: Blue, Red, and Purple. They guide Olimar to a cave, where all the Pikmin live. However, they are in constant fear of the Bulborb, a race of giant creatures that feast on the Pikmin. The Pikmin reveal to Olimar a piece of his ship that they found. Olimar realizes that if he finds each piece he can repair his ship, and go back home.
Meanwhile, Louie awakens on a giant tree branch, millions of feet above the ground. He screams in terror, and slips off of the branch. However, a bunch of Pikmin gather around to catch Louie. Louie is horrified and runs off, but the Pikmin won't leave him alone. Eventually, he accepts what has happened to him and follows the Pikmin to their home, a tiny hole in the side of a small dirt hill. He crawls in and the Pikmin show him a piece of his ship they found. Louie comes to the same realization Olimar did, and so he sets out to find the rest of the ship.
Olimar and the Pikmin arrive at a huge waterfall, where several Bulborbs are swimming around. The Pikmin all hold hands and form a little rope for Olimar to shimmy down. Olimar sneaks past the Bulborbs, and finds a piece of the ship. He is about to reach for it when a sleeping Bulborb rolls over on top of it. The Pikmin join together in the shape of a stick so Olimar can stick it under the Bulborb and move it over. Olimar grabs the piece, and they run off, but are spotted. The Bulborb roars at them and the whole pack chases them off into the forest, where the Bulborbs eventually lose sight of them. Olimar and his pack of Pikmin see another tiny part of the ship, but another Pikmin picks it up before they can. The Pikmin runs off and they chase after it to get the piece back, but run into Louie, who the Pikmin gives the piece to. Olimar and Louie renuite, and Olimar tells Louie they already found a few pieces.
That night, they have a bonfire at the Pikmin's cave, and Louie and Olimar put back together the pieces they have already. The next day, Louie wakes up and sees Olimar cooking something on the fire. At first Louie is shocked because he thinks Olimar is cooking a Pikmin, but it turns out to be meat from a dead Bulborb he found. Louie takes a bite but it tastes disgusting, so Olimar adds some fruit and stuff for flavoring. Louie decides he's not hungry and goes out to look for more parts. Louie is walking around when he sees a large sleeping worm creature, known as the Sandbelching Meerslug. The Meerslug attacks Louie, and tries eating him, but Olimar and a bunch of Pikmin show up to save him. As they run off, the Meerslug begins to cough and spits out a spaceship part, then goes back to sleep.
After a montage of Olimar and Louie collecting parts for the ship, we see them in the cave again, and they discover they only have three parts left, the engine and two rocket boosters. After a long climb up the Great Mountain, the one place they haven't searched. They are walking along a trail when they hear a rumbling noise. Olimar looks up and sees there is an avalanche coming their way. Olimar and Louie jump out of the way and begin to slide down the mountain. Olimar is buried under the landslide, and Louie falls into a pit as the landside comes down and caves in the hole. Louie is trapped, and it looks like all is lost.
A few weeks later, Olimar wakes up back at the Pikmin cave, and sees only three Pikmin are left there. They show Olimar the last three pieces, the engine and the two rocket boosters. Olimar says it's useless without Louie to help him. Suddenly, Olimar gets an idea. He takes apart the ship as all the Pikmin watch, and rebuilds into a small plane for him to fly. He takes off in the plane, and activates the rocket boosters, launching him off at sonic speed. Back at the mountain, Louie is starving, when he hears a crash noise. The cave begins to collapse in on itself, so he runs off and takes cover in a tunnel. He finds a dead end where a boulder blocks the way, but he manages to kick it out of place and escapes as the entire mountain collapses to the ground. He looks up and sees Olimar in the plane. Olimar gives Louie a thumbs up and flies down to rescue him.
However, several Bulborbs come up from the rubble of the mountain and attack them. Olimar and Louie fly away, as the Bulborbs on the ground follow them in hot pursuit. Olimar and Louie eventually arrive back at the Pikmin's cave, where the two take apart the plane and rebuild it. However, the Bulborbs arrive and all the Pikmin begin panicking. Olimar and Louie manage to quickly build a small tank and shoot at the Bulborbs, scaring them all off. That night, at the last bonfire, all the Pikmin are gathered for a Farewell Party as the ship has finally been rebuilt. Olimar and Louie say their goodbyes, and take off once and for all, hopefully to one day return to their homeworld.
After the credits, we see a huge crowd of people gathered in a temple, chanting ominously as a blue flash of light appears before them, and out of it comes Master Hand...
- Jim Carrey - Olimar
- Jason Ritter - Louie
- Tim Curry - Crazy Old Stranger